During the first fight in the film Neo is confronted with three Agents and when they appear clearly faster than before he observes wryly, “Upgrades.” They don’t last long, however, and its also the last time in the film that Neo will fight Agents. Much more interesting is that his archenemy has become his nemesis. No full explanation is given, but good old Agent Smith is back. Having been destroyed by Neo, he has instead been “set free” and is no longer an Agent of the system. The suggestion is that “perhaps some code was copied or overwritten”: in other words, when Neo destroyed the original Agent Smith some of the base computer code which comprises everyone in the Matrix was altered and Agent Smith acquired some part of Neo’s uniqueness. And this uniqueness has transformed into multiplicity: his freedom from the system has given him the ability to overwrite the code of others himself, be they ordinary civilians, rebels or indeed other Agents. He tries to pull the same trick on Neo, but nothing is ever that simple: Neo, after all, is The One. But the impression is that, if Smith could defeat Neo and “overwrite his code” he would assimilate much (if not all) of Neo’s power and become an Anti-One. The net result is that Agent Smith, at this point, is invincible. We are treated to a fight scene in which increasing numbers of Smiths arrive, eventually numbering a hundred or so. Echoes of the Hydra myth of Greek mythology, maybe, where when one head is cut off, two grow back to replace it. In the myth, you had to quickly cauterise the wound with fire before the heads can regenerate; Neo needs some such fire but lacks it at the moment. In the end he does what Cypher advised in the first film and runs. We bump into Smith again a couple of times in the film, but if you stayed and watched the credits to the end, you’ll have seen the trailer for the third film and know that Smith is being set up to be the big baddie there (“If you can’t defeat him tonight, tomorrow it will be too late”).
We are also introduced to another group of programmes (?people?) with more autonomy than your average Agent. We learn that The Oracle of the first film is one such programme, along with her bodyguard ?Seriph? (who seems to play a part in the third film) and a strange character called The Merovingian. He has kidnapped The Keymaker, who our intrepid heroes need in order to fulfill the prophecy that, when The One reaches the Core (of the computer system), the war will be over. Thus ensues a great deal of fighting, the good guys eventually winning.
What is interesting here is that, in contrast to the first film where there are simply good guys and bad guys, in the second film there are at least four groups of antagonists: the rebels, the Agents, Smith(s) and independents like The Merovingian. While some are clearly good and some bad, others are ambiguous and others may simply stand for chaos and fight everyone. The result is a much more complex set of motivations and relations which does the film no end of good, and I’m sure will be further developed in the third part of the trilogy.
At the end of the film (which was more conclusive than I’d imagined it would be) Neo does reach the Core and meets a perhaps rather too god-like chap called The Architect. They have an extraordinarily complex conversation which throws more than one spanner in the works. The story moves to a meta-level, where the rebellion against the machines is actually part of the programme, and has indeed been run five times before. The One is an integral part of the programme, basically allowing it to be rebooted (which, I take it, is what was meant by “the war will be over”). As far as I understand it, the idea is this: as Agent Smith said in the original film, the human mind rejected the first Matrix because it was too perfect, and ever since the machines have been updating and refining the programme until it reaches a tolerable level of efficiency. If The Architect is the father of the Matrix, The Oracle is its Mother: she (the programme) realised that at about 99% of the time the human mind would accept the Matrix if it was given a choice at even a sub-conscious level. However, the 1% that did not would become increasingly dangerous as their numbers expanded. So the machines introduced The One, who would be able to lead the rebels onwards with hope, until the reached the point of directly challenging the core of the system, whereupon they would unwittingly reboot the system and restart the whole (now refined process) from the beginning. Next time, however, only 0.5% would reject the Matrix, then 0.25% and so on. This is, as I said, the sixth time the programme has been run, which explains why The Oracle knows what will happen in the future: because it already has five times. It also casts her role in the in the first film in a somewhat different light: she is doing research into all the “potentials” which we see in her flat, such as the boy with the spoon, in order to improve the Matrix programme so that these anomalies do not arise next time. And don’t forget that Morpheus said that The Oracle freed the first of the rebels; to facilitate the research, it seems. Hence the entire underground uprising is anticipated and planned by the machines, more or less like keeping a database of software bugs.
At the end of meeting with The Architect, Neo is given a choice: go through the door on the left and save the entire human population (by rebooting the programme), or go through the door on the left and save the life of Trinity (who has just been shot by an Agent). Love-struck as he is, Neo chooses to save Trinity, but by this stage in the game we’ve no idea whether that was indeed what he was meant to do. Trinity dies (as was prophesied, but since she dies within the Matrix, Neo is able to give her code a little tweak and in effect give her the kiss of life. They return to the Nebuchcadnezzar and Neo tells Morpheus some of what happened (I think he left out the bit about the sixth run, though) and Morpheus, understandably, has a crisis of faith. He has lived by the Prophecy all his life and now it has not come true: the war is not over even though The One reached the Core. Then we are treated to yet another twist: Sentinels turn up and ambush the ship and it is destroyed by a bomb (looked more like a missile to me, though). The crew escape, are about to be killed by the Sentinels when Neo stops, saying that “something has changed”, turns round to face the Sentinels and, rather as he does with bullets, stops them dead in their tracks. The Sentinels short-circuit and crash to the ground; Neo follows them, the physical exertion being too much. And that, pretty much, is the end of the film (I’m purposefully leaving out the odd spoiler).
What is going on here? When Neo faces the Sentinels, it is not in the Matrix but in the “real” world, although he appears to have Matrix-like powers, even if their physical toll is extremely great. I see two possibilities here, which have quite different implications. One is that this supposedly “real” world of the Sentinels, the hovercraft and Zion is all in fact part of a deeper meta-programme. What we have previously know as the Matrix is in truth a Matrix-within-a-Matrix, rather like a Russian doll, and everything we have seen so far in the films has been within this meta-programme: we have not yet seen the “real” world. People living wiithin the Matrix believe it is real; those who have escaped the Matrix believe that they have escaped to reality, but that would be seen to be just as false, if only they could escape to the next level, and it could be that Neo is beginning that escape. The story of meta-Matrixes, however, could go on to infinity. Alternatively, it could be that the borders between the Matrix and the non-Matrix worlds is becoming blurred; there is a “strange loop” (to use Douglas Hofstadter’s phrase from Gödel, Escher, Bach) between the worlds, such that Neo will be increasingly able to use Matrix-like powers within the world of the machines and that the conclusion of the trilogy will involve these powers. This does not have to be a contradiction in the logic of the film. One explanation is that it occurs as a by-product of the increasing refinement of the Matrix. In The Architect’s constant striving for efficiency in the system, The One will become correspondingly efficient, perhaps in ways unforeseen. And it could be do do with the bond with Smith: Smith has become free from the bounds of the machines and is able to inhabit human minds from his encounter with Neo, and in a parallel way Neo has become able to “feel” (his word) and control the machines. I’m tempted to go this way: we’re not watching the third incarnation of The One, because that went according to plan (from the machines’ point of view), but the sixth, because in the end it doesn’t go according to plan. And the bond with Smith seems the most likely source of that at this point.